Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.

        Load Settings

        Choose a saved report profile from the dropdown box below:

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.26

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-04-01, 12:36 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data

        nf-core/quantms Software Versions

        nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms

        Process Name Software Version
        CONSENSUSID ConsensusID 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        EXTRACTPSMFEATURES PSMFeatureExtractor 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        FDRCONSENSUSID FalseDiscoveryRate 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        FILEMERGE FileMerger 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDCONFLICTRESOLVER IDConflictResolver 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDFILTER IDFilter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDMAPPER IDMapper 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        ISOBARICANALYZER IsobaricAnalyzer 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MSSTATSCONVERTER MSstatsConverter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MSSTATSTMT bioconductor-msstatstmt 2.2.0
        r-base 4.1.1
        PERCOLATOR PercolatorAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        percolator 3.05.0, Build Date Aug 31 2020 19:03:04
        PROTEININFERENCER ProteinInference 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        PROTEINQUANTIFIER ProteinQuantifier 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        SEARCHENGINECOMET Comet 2019.01 rev. 5
        CometAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        SEARCHENGINEMSGF MSGFPlusAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        msgf_plus MS-GF+ Release (v2021.03.22) (22 March 2021)
        THERMORAWFILEPARSER ThermoRawFileParser 1.3.4
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms

        Core Nextflow options

        runName
        loving_cajal
        containerEngine
        singularity
        launchDir
        /hps/nobackup/juan/pride/reanalysis/PXD020248
        workDir
        /hps/nobackup/juan/pride/reanalysis/PXD020248/work
        projectDir
        /hps/nobackup/juan/pride/reanalysis/quantms
        userName
        pst_prd
        profile
        ebiclusters
        configFiles
        /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config, /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config

        Input/output options

        input
        PXD020248-TMT.sdrf.tsv
        outdir
        PXD020248-TMT
        root_folder
        /hps/nobackup/juan/pride/reanalysis/PXD020248/
        local_input_type
        raw

        Protein database

        database
        /hps/nobackup/juan/pride/reanalysis/multiomics-configs/databases/Homo-sapiens-uniprot-reviewed-isoforms-contaminants-decoy-202105.fasta

        Database search

        search_engines
        comet,msgf
        instrument
        N/A

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Max job request options

        max_cpus
        48
        max_memory
        300 GB
        max_time
        10d

        Generic options

        hostnames
        N/A

        MultiQC v1.26 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.